CellWhere: graphical display of interaction networks organized on subcellular localizations.

Lu Zhu, Apostolos Malatras, Matthew Thorley, Idonnya Aghoghogbe, Arvind Mer, Stephanie Duguez, Gillian Butler-Browne, Thomas Voit, William Duddy

    Research output: Contribution to journalArticle

    Abstract

    Given a query list of genes or proteins, CellWhere produces an interactive graphical display that mimics the structure of a cell, showing the local interaction network organized into subcellular locations. This user-friendly tool helps in the formulation of mechanistic hypotheses by enabling the experimental biologist to explore simultaneously two elements of functional context: (i) protein subcellular localization and (ii) protein-protein interactions or gene functional associations. Subcellular localization terms are obtained from public sources (the Gene Ontology and UniProt-together containing several thousand such terms) then mapped onto a smaller number of CellWhere localizations. These localizations include all major cell compartments, but the user may modify the mapping as desired. Protein-protein interaction listings, and their associated evidence strength scores, are obtained from the Mentha interactome server, or power-users may upload a pre-made network produced using some other interactomics tool. The Cytoscape.js JavaScript library is used in producing the graphical display. Importantly, for a protein that has been observed at multiple subcellular locations, users may prioritize the visual display of locations that are of special relevance to their research domain. CellWhere is at http://cellwhere-myology.rhcloud.com.
    LanguageEnglish
    PagesW571-W575
    JournalNucleic Acids Research
    Volume43
    Issue numberW1
    Early online date16 Apr 2015
    DOIs
    Publication statusE-pub ahead of print - 16 Apr 2015

    Fingerprint

    Proteins
    Mentha
    Gene Ontology
    Libraries
    Research
    Genes

    Keywords

    • Muscle
    • Subcellular localization
    • graphical display
    • protein-protein interction

    Cite this

    Zhu, Lu ; Malatras, Apostolos ; Thorley, Matthew ; Aghoghogbe, Idonnya ; Mer, Arvind ; Duguez, Stephanie ; Butler-Browne, Gillian ; Voit, Thomas ; Duddy, William. / CellWhere: graphical display of interaction networks organized on subcellular localizations. In: Nucleic Acids Research. 2015 ; Vol. 43, No. W1. pp. W571-W575.
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    abstract = "Given a query list of genes or proteins, CellWhere produces an interactive graphical display that mimics the structure of a cell, showing the local interaction network organized into subcellular locations. This user-friendly tool helps in the formulation of mechanistic hypotheses by enabling the experimental biologist to explore simultaneously two elements of functional context: (i) protein subcellular localization and (ii) protein-protein interactions or gene functional associations. Subcellular localization terms are obtained from public sources (the Gene Ontology and UniProt-together containing several thousand such terms) then mapped onto a smaller number of CellWhere localizations. These localizations include all major cell compartments, but the user may modify the mapping as desired. Protein-protein interaction listings, and their associated evidence strength scores, are obtained from the Mentha interactome server, or power-users may upload a pre-made network produced using some other interactomics tool. The Cytoscape.js JavaScript library is used in producing the graphical display. Importantly, for a protein that has been observed at multiple subcellular locations, users may prioritize the visual display of locations that are of special relevance to their research domain. CellWhere is at http://cellwhere-myology.rhcloud.com.",
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    Zhu, L, Malatras, A, Thorley, M, Aghoghogbe, I, Mer, A, Duguez, S, Butler-Browne, G, Voit, T & Duddy, W 2015, 'CellWhere: graphical display of interaction networks organized on subcellular localizations.', Nucleic Acids Research, vol. 43, no. W1, pp. W571-W575. https://doi.org/10.1093/nar/gkv354

    CellWhere: graphical display of interaction networks organized on subcellular localizations. / Zhu, Lu; Malatras, Apostolos; Thorley, Matthew; Aghoghogbe, Idonnya; Mer, Arvind; Duguez, Stephanie; Butler-Browne, Gillian; Voit, Thomas; Duddy, William.

    In: Nucleic Acids Research, Vol. 43, No. W1, 16.04.2015, p. W571-W575.

    Research output: Contribution to journalArticle

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    AU - Zhu, Lu

    AU - Malatras, Apostolos

    AU - Thorley, Matthew

    AU - Aghoghogbe, Idonnya

    AU - Mer, Arvind

    AU - Duguez, Stephanie

    AU - Butler-Browne, Gillian

    AU - Voit, Thomas

    AU - Duddy, William

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    KW - graphical display

    KW - protein-protein interction

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    ER -